Overview of The Pathway Tools Software

What is a Pathway/Genome Database and What is Pathway Tools?

A PGDB is a bioinformatics DB that integrates genomic data with
detailed functional annotations of the genome, such as descriptions of
metabolic and signalling pathways, and of the regulatory network.
The EcoCyc and HumanCyc DBs are PGDBs (see EcoCyc.org and
HumanCyc.org).

A PGDB serves as a central resource for
capturing, integrating, and disseminating new scientific findings
about the organism. It is a vehicle for tracking the
evolving annotation of the genome, metabolic network, and genetic
network of the organism, and for communicating that evolving knowledge
through the Web. All genome annotations produced to date are
incomplete, and contain significant numbers of errors. For organisms
with active experimental communities, ongoing efforts are required to
update those annotations to reflect new computational inferences, and
new gene identifications and pathways reported in the experimental
literature.

The existence of an up-to-date genome annotation for an organism is a
prerequisite for performing functional genomics studies of an organism
because (a) one aim of functional genomics is to determine the functions
of genes whose function is not already known, therefore, functional
genomics efforts require access to the most accurate genome annotation
possible; (b) the extensive new knowledge about gene function and gene
regulation that will be gleaned from functional genomics studies must be
integrated and disseminated to the scientific community, such as through
a PGDB.

Pathway Tools supports creation, editing, querying,
visualization, and analysis of PGDBs. The software also allows users to
publish a PGDB on the Web for access by the scientific community.

The Bioinformatics datatypes supported by the Pathway/Genome Navigator component of Pathway Tools are
listed below. For each of the datatypes , Pathway Tools provides
querying capabilities, visualization tools (such as for drawing pathways
and genome maps), and interactive editing tools to allow users to update
data (such as modifying a metabolic pathway or defining a new DNA
binding site for a transcription factor).
The visualization and querying capabilities allow PGDBs to be published
on the Web, or to be accessed as a desktop application on the PC, Mac, and Linux platforms.
The desktop and Web capabilities of the software overlap substantially, with some
differences
[details].

Pathway/Genome Navigator: Analysis of Large-Scale Datasets

Pathway Tools can aid analyses of gene expression, protein
expression, and metabolomics experiments through the Pathway Tools
Omics Viewers, which allow omics datasets to be graphically painted
onto three system-level diagrams: a diagram of the full metabolic
network of the organism, a diagram of the full regulatory network of
the organism, and a diagram of the full genome of the organism. The
software can produce animated displays of a series of omics
measurements. It can also depict data from multiple omics datatypes
simultaneously, such as mixing gene-expression and metabolomics data
on one diagram.

Click on images to see full-size.

Other Pathway Tools capabilities for analysis of large-scale datasets include:

The Omics Dashboard provides a system-oriented view of omics datasets,
enabling the user to view aggregate responses of cellular systems such as biosynthesis
and DNA repair, and responses and the pathway and gene levels:

The MetaFlux component of Pathway Tools supports development and execution of steady-state metabolic
flux models using flux-balance analysis. Its gap filler module accelerates model development by
suggesting improvements to a model such as addition of missing reactions. Reaction fluxes computed
by MetaFlux can be painted onto the metabolic map diagram to speed understanding of modeling results.
MetaFlux can simulate gene knock outs for selected genes, or for all genes in the organism.

Pathway Tools includes a suite of interactive editing tools for
adding new information to a PGDB, and for updating existing information.
Tools such as a pathway editor, gene editor, and enzyme editor speed
database development.

Other Aspects of Pathway Tools

Pathway Tools has a large user community, who have already successfully
used the software to create database for many organisms.